Merge branch 'INCF:main' into movefile

.github/dependabot.yml

@@ -0,0 +1,13 @@
+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+  - package-ecosystem: 'github-actions'
+    directory: '/'
+    schedule:
+      interval: 'monthly'
+
+  - package-ecosystem: 'gitsubmodule'
+    directory: '/'
+    schedule:
+      interval: 'monthly'

.github/workflows/publishdocs.yaml

@@ -0,0 +1,20 @@
+---
+name: Publish docs via GitHub Pages
+on:
+  push:
+    branches:
+    - main
+
+jobs:
+  build:
+    name: Deploy docs
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'INCF'
+    steps:
+    - name: Checkout master
+      uses: actions/checkout@v4
+
+    - name: Deploy docs
+      uses: mhausenblas/mkdocs-deploy-gh-pages@master
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/update_spreadsheet.yml

@@ -0,0 +1,46 @@
+name: Update spreadsheet
+
+on:
+  push:
+    branches: [ main ]
+
+  # to trigger update manually from the Action tab in github
+  workflow_dispatch:
+    inputs:
+      log:
+        description: "convert spreadsheet"
+        required: false
+
+jobs:
+  update_spreadsheet:
+
+    runs-on: ubuntu-latest
+
+    if: github.repository_owner == 'INCF'
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        make install
+
+    - name: Convert table
+      run: make convert
+
+    # if there have been changes,
+    # a PR is created using the checkout branch for this workflow
+    # https://github.com/peter-evans/create-pull-request
+    - name: Create Pull-Request
+      uses: peter-evans/create-pull-request@v5
+      with:
+        commit-message: Update spreadsheets
+        delete-branch: true
+        title: 'MNT: Update spreadsheets'

.github/workflows/validate.yml

@@ -0,0 +1,49 @@
+name: validate jsonld
+
+on:
+  push:
+    branches:
+      - master
+      - main
+      - dev
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    if: github.repository_owner == 'INCF'
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      - name: Setup Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "12.x"
+
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      # Checks that our JSON are valid
+      - name: Check for syntax errors
+        run: |
+          npm install -g jsonlint
+          grep -r  "@context" schemas | cut -d: -f1 | xargs -I fname jsonlint -q fname
+
+      # Checks that the schemas are valid
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install reproschema requests_cache
+
+      - name: Test with pyshacl
+        run: |
+          reproschema -l DEBUG validate schemas/artemis/protocols
+          reproschema -l DEBUG validate schemas/artemis/activities
+          reproschema -l DEBUG validate schemas/artemis/artemis_schema.jsonld

.gitignore

@@ -0,0 +1,133 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+.DS_Store
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Pycharm
+.idea/

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: check-yaml
+    -   id: check-added-large-files
+
+-   repo: https://github.com/psf/black
+    rev: "22.6.0"
+    hooks:
+    -   id: black
+
+-   repo: https://github.com/asottile/reorder_python_imports
+    rev: "v3.8.2"
+    hooks:
+        - id: reorder-python-imports

.vscode/extensions.json

@@ -0,0 +1,7 @@
+{
+    "recommendations": [
+        "ms-python.vscode-pylance",
+        "sourcery.sourcery",
+        "ms-python.python"
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "makefile.extensionOutputFolder": "./.vscode"
+}